Rojas-Villalobos Camila, Ossandon Francisco J, Castillo-Vilcahuaman Camila, Sepúlveda-Rebolledo Pedro, Castro-Salinas David, Zapata-Araya Abraham, Arisan Dilanaz, Perez-Acle Tomás, Issotta Francisco, Quatrini Raquel, Moya-Beltrán Ana
Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago 8580704, Chile.
Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Santiago 8420524, Chile.
Nucleic Acids Res. 2025 Jul 7;53(W1):W398-W407. doi: 10.1093/nar/gkaf396.
Horizontal gene transfer plays a critical role in microbial genome evolution and adaptation. Integrated foreign DNA fragments encompass various types of mobile genetic elements (MGEs), ranging from small transposons to conspicuous integrative and conjugative elements. These regions often confer advantageous traits, including antibiotic resistance or novel metabolic capabilities, and contain foreign sequence signatures and hallmark genes such as transposases, integrases, etc. While bioinformatic tools target specific MGE subsets using alignments, compositional signatures, or diagnostic gene mapping, no single platform offers a unified framework for comprehensive, evidence-based, MGE identification and classification. To address this challenge, we developed MOBHunter, an advanced bioinformatic pipeline that consolidates standalone tools and in-house algorithms. Unlike basic tool concatenation, MOBHunter yields consensus identifications, score-supported classifications, and enhanced web visualizations. The platform reduces end user analysis time by integrating data collection, processing, and interpretation into a unified workflow. It delivers robust classifications of MGEs into distinct families and provides a comprehensive overview of the flexible regions of any given input genome. URL: https://informatica.utem.cl/mobhunter/.
水平基因转移在微生物基因组进化和适应过程中起着关键作用。整合的外源DNA片段包含各种类型的可移动遗传元件（MGEs），从小的转座子到明显的整合和接合元件。这些区域通常赋予有利的性状，包括抗生素抗性或新的代谢能力，并包含外源序列特征和标志性基因，如转座酶、整合酶等。虽然生物信息学工具使用比对、组成特征或诊断基因图谱来靶向特定的MGE子集，但没有一个单一的平台能为基于证据的全面MGE识别和分类提供统一的框架。为应对这一挑战，我们开发了MOBHunter，这是一种先进的生物信息学流程，它整合了独立工具和内部算法。与基本的工具串联不同，MOBHunter能产生一致的识别结果、有分数支持的分类以及增强的网络可视化。该平台通过将数据收集、处理和解释整合到一个统一的工作流程中，减少了终端用户的分析时间。它能将MGEs可靠地分类到不同的家族中，并提供任何给定输入基因组灵活区域的全面概述。网址：https://informatica.utem.cl/mobhunter/ 。
